RNA Detection

file name prefix is x. The following are a preferred set of file

name conventions. Having standard file names makes the man-

agement of files easier.

x.fastq.gz: zipped raw data x_trim3.fastq: after removing the 3^0

end adapter sequencesx_trim3_nodup.fastq: after removing PCR

duplicatesx_trim3_nodup_bcnn.fastq: split libraries with barcode

nn, such as 01, 02...x_trim_nodup_bcnn.fastq: after removing 5^0

PARIS data (fastq)

Chimerc.out.sam

Chimeric.out.junction

DG, XG, and NG groups

PARIS data (fastq)

Aligned.out.sam

(non-gapped and gapped)

Gapped primary reads

Remove adapters

Remove PCR duplicates

Split libraries

STAR map

to genomes

Remove secondary
alignments and non-
gapped reads

Remove spliced reads

and define read groups

Inter-molecular groups Intra-molecular groups (sam

file and read group)

IGV visualization

Phylogenetic analysis:

alignment based

RNA-RNA interactions

Chimerc.out.sam

Chimeric.out.junction

STAR map to curated

RNA references

Do not use normal

aligned reads

Visualize interactions

Alternative structures

Phylogenetic analysis:

direct comparison

Fig. 4The PARIS analysis pipeline, modified from the PARIS paper [21]. Major analyses outlined here include
DG and NG assembly, visualization of RNA structure data and models in IGV, two approaches of phylogenetic
analysis, analysis of alternative structures, identification and visualization of RNA–RNA interactions

74 Zhipeng Lu et al.